HIV and HCV viruses form long-term relationships with the host leading to chronic infection, and in turn, are expected to experience selective pressure driven by host's immune system that promotes immune escape and evasion. However, relative contribution of different immune responses to the evolution of these viruses is unclear. This Academic Research Enhancement Award (AREA) R15 proposal is focused on detailed evolutionary analysis of escape sequence changes to address the following Specific Aims. (1) To uncover relative contribution of cell-mediated (such as CTL-driven and T helper-driven) and humoral (via neutralizing antibodies) responses of the host's immune system on the evolution of HIV and HCV viruses. Pattern of sequence changes at different kinds of epitopes (both linear and non-linear) will be studied, including the extent of synonymous and nonsynonymous substitutions and distribution of convergent and parallel amino acid changes, to delineate relative role of immune responses and to determine which response plays the larger role. Identification of epitopes with many escape changes (that can be attributed to the immune response- driven selection) and those with little or no escape changes (despite long-term interactions with the immune system due to strong functional constraints) will provide important insights for the design of novel vaccines and treatments. (2) To study short-term and long-term evolutionary fate of escape mutations in epitopes of HIV and HCV. Evolution of escape mutations will be studied to uncover their evolutionary contribution to the short-term and long-term evolution of viruses, and whether the same escape mutations can be successful in different hosts and have the potential to propagate throughout global viral population. This will provide novel insights into the evolutionary and functional consequences of escape mutations found within individual hosts, and also will pinpoint different categories of escape mutations (such as those with detrimental effect on viral fitness). In summary, this study will yield novel insights into the role of selection exerted by the host's immune system and factors that drive short- and long-term evolution of viruses. Our findings will help to elucidate fundamental processes of host-pathogen interactions and to delineate mechanisms of viral evolution. Results of this project will establish foundation for future 3D structural studies of epitope-MHC binding and interactions, and will provide a list of escape-prone epitopes for longitudinal studies linking specific genomic sequence changes with clinical data and strength of the immune response. PUBLIC HEALTH RELEVANCE: In chronic infections caused by HIV and HCV viruses, both cell-mediated and humoral responses play a role;however, their relative contribution to evolution of immune escape in these highly infectious viruses remains unclear. Our goal is to analyze patterns of evolutionary sequence changes to delineate relative roles of T helper-driven, CTL-driven and humoral immune responses as underlying factors of virus evolution. These results can be used in the development of novel vaccines and treatments and will lead to better understating of host- pathogen interactions.